Contacts of the helix formed by residues 298 - 310 (chain B) in PDB entry 6PUO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 298 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241B VAL* 3.9 31.7 - - + +
242B ALA* 4.6 2.5 - - - -
243B THR* 4.0 11.6 + - - +
287B VAL* 3.7 15.7 - - + -
296B GLY* 3.2 1.7 - - - -
297B VAL* 1.3 79.1 - - - +
299B ILE* 1.3 65.7 + - + +
300B PRO 3.6 0.2 - - - -
301B LEU* 3.5 4.8 + - - +
302B ARG* 3.1 26.0 + - + +
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Residues in contact with ILE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B GLY* 3.9 23.8 - - - +
298B GLU* 1.3 77.5 - - + +
300B PRO* 1.3 68.8 - - + +
301B LEU 3.2 0.7 + - - -
302B ARG* 3.3 14.7 + - + +
303B THR* 3.4 26.5 + - + +
339B THR* 6.0 7.4 - - + +
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Residues in contact with PRO 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B GLN* 4.4 14.4 - - - +
296B GLY 3.8 9.0 - - - +
297B VAL* 3.5 15.9 - - - +
299B ILE* 1.3 91.2 - - + +
301B LEU* 1.3 55.4 + - - +
303B THR* 3.8 6.0 + - + +
304B ARG* 3.1 33.3 + - - +
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B VAL* 4.5 3.8 - - + -
146B SER 4.1 6.7 - - - +
147B GLN* 3.4 25.9 - - - +
149B THR* 4.4 16.6 - - - +
154B ILE* 4.3 17.9 - - + -
241B VAL* 5.3 7.6 - - + -
285B ILE* 5.4 5.2 - - + -
287B VAL* 3.8 31.2 - - + -
297B VAL 4.7 2.4 + - - +
298B GLU 3.5 7.2 + - - +
299B ILE 3.2 0.8 - - - -
300B PRO* 1.3 78.2 - - - +
302B ARG* 1.3 62.9 + - - +
303B THR 3.3 0.7 - - - -
304B ARG* 3.4 21.5 + - - +
305B LEU* 2.9 37.2 + - + +
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Residues in contact with ARG 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B SER* 3.3 13.9 + - - -
173B VAL 3.1 27.3 + - - -
174B THR* 4.7 9.3 + - - +
206B ILE* 3.3 31.8 + - + +
207B THR* 3.6 8.1 + - - +
208B GLY* 3.9 15.8 - - - +
241B VAL* 4.8 18.6 - - + -
298B GLU* 3.1 20.5 + - - +
299B ILE* 3.3 8.0 + - - +
301B LEU* 1.3 80.7 - - - +
303B THR* 1.3 60.1 + - + +
305B LEU* 3.4 6.5 + - - +
306B GLU* 2.9 47.0 + - - +
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Residues in contact with THR 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ILE* 3.4 28.3 + - + +
300B PRO* 3.8 9.4 + - - +
302B ARG* 1.3 78.7 - - + +
304B ARG* 1.3 62.3 + - - +
306B GLU* 3.4 10.6 + - - +
307B LYS* 2.9 29.9 + - - +
339B THR* 6.4 2.0 - - + -
342B ASN* 5.3 11.2 - - - +
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Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B GLN* 3.8 23.4 + - - +
148B ASP* 4.1 14.1 - - - +
149B THR 3.6 16.2 + - - -
150B PRO* 5.1 1.4 - - - +
151B SER* 4.4 15.2 + - - +
300B PRO* 3.1 24.9 + - - +
301B LEU* 3.4 21.2 + - - +
302B ARG 3.3 0.4 - - - -
303B THR* 1.3 86.5 + - - +
305B LEU* 1.3 58.3 + - - +
307B LYS* 3.4 11.9 + - - +
308B PHE* 2.9 30.5 + - - +
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Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B SER* 4.0 31.4 - - - +
154B ILE* 4.5 22.0 - - + -
155B TYR* 5.1 1.6 - - + +
158B MET* 4.8 13.0 - - + -
206B ILE* 4.6 18.2 - - + -
239B ILE* 4.9 7.4 - - + -
241B VAL* 5.3 4.9 - - + -
285B ILE* 5.1 5.6 - - + -
301B LEU* 2.9 30.4 + - + +
302B ARG* 3.7 5.6 - - - +
303B THR 3.3 0.2 - - - -
304B ARG* 1.3 76.3 - - - +
306B GLU* 1.3 58.1 + - + +
308B PHE* 3.3 1.6 + - + -
309B ILE* 2.9 51.1 + - + +
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B LEU* 4.3 14.0 - - + +
172B SER* 3.3 26.1 + - - -
206B ILE* 4.2 16.3 - - + +
302B ARG* 2.9 50.3 + - - +
303B THR* 3.7 8.7 - - - +
304B ARG 3.3 0.2 - - - -
305B LEU* 1.3 76.7 - - - +
307B LYS* 1.3 56.8 + - - +
309B ILE* 3.4 2.4 + - - +
310B SER* 2.9 30.7 + - - -
325B ILE* 3.8 26.8 - - + +
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Residues in contact with LYS 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B THR 2.9 17.8 + - - +
304B ARG* 4.0 11.0 - - - +
306B GLU* 1.3 77.0 - - - +
308B PHE* 1.3 61.7 + - - +
310B SER* 3.3 15.9 + - - +
311B GLU* 3.3 35.3 - - - +
325B ILE* 5.9 0.2 - - - -
346B ASN* 5.2 13.2 - - + +
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Residues in contact with PHE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B SER* 3.3 33.0 - - - +
152B SER* 3.7 34.3 - - - -
155B TYR* 3.7 26.5 - + + -
304B ARG 2.9 14.8 + - - +
305B LEU* 3.9 3.1 - - + +
307B LYS* 1.3 75.5 - - - +
309B ILE* 1.3 69.7 + - + +
311B GLU* 3.4 14.2 + - - +
312B GLN* 2.9 52.9 + - + -
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Residues in contact with ILE 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B TYR* 4.1 20.6 - - + -
158B MET* 4.3 8.3 - - + -
167B PRO* 5.1 4.7 - - + -
170B LEU* 3.9 31.4 - - + -
204B TRP* 4.1 27.4 - - + -
206B ILE* 6.1 2.7 - - + -
239B ILE* 6.3 1.1 - - + -
305B LEU* 2.9 45.0 + - + +
306B GLU* 3.9 3.4 - - - +
308B PHE* 1.3 77.9 - - + +
310B SER* 1.3 59.3 + - - +
311B GLU 3.0 6.1 + - - -
312B GLN* 3.3 15.9 + - - +
323B ILE* 3.8 26.4 - - + +
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Residues in contact with SER 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B LEU* 5.5 1.3 - - - -
306B GLU 2.9 15.5 + - - -
307B LYS* 3.3 18.1 + - - +
308B PHE 3.2 0.4 - - - -
309B ILE* 1.3 76.9 - - - +
311B GLU* 1.3 60.0 + - - +
312B GLN 3.8 0.4 - - - -
322B LYS* 4.7 9.7 + - - +
323B ILE* 3.6 25.0 + - - +
325B ILE* 3.7 31.7 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il